MolNFT v1 · #52501 · protein

PCSK9-deltac D374Y mutant bound to wt EGF-a of ldlr

2W2O · Proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9-deltac D374Y mutant bound to wt EGF-a of ldlr”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.34). MolNFT v1 #52501 on GenesisL1: 3D structure, binding sites…

PDB: 2W2O
Type: protein
Length: 413 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proprotein convertase SUBTILISIN/KEXIN type 9; Low-density lipoprotein receptor
EC: 3.4.21.-
UniProt: Q8NBP7, P01130
Ligands: CA
Pockets: 4 · best druggability 0.34

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	274	31% helix, 23% strand	Q8NBP7
E	Low-density lipoprotein receptor	protein	47	9% helix, 30% strand	P01130
P	Proprotein convertase SUBTILISIN/KEXIN type 9	protein	92	29% helix, 39% strand	Q8NBP7

Ligands and binding sites

CA · Calcium ion · metal · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	92	0.34	0.74	15	empty
2	63	0.31	0.75	14	empty
3	58	0.28	0.74	17	empty
4	61	0.28	0.74	17	empty

Interfaces

2 interfaces between chains.

A–P · 1300 Å² buried · 28 hydrogen bonds · protein-protein
A–E · 562 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

2W2O · PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR · the same entry in another collection · chain A against A, TM-score 1.00
P01130 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor (P01130) · a predicted model of the same protein · chain E against A, TM-score 0.85

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8NBP7
Every structure of UniProt P01130
Elsewhere: RCSB PDB 2W2O · PDBe 2W2O · UniProt Q8NBP7 · UniProt P01130

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.